X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=fe6f4cf9eed7610eaf88a1a30d02fa06fd67ede1;hb=52c2c3879d5dc5e7b4ba7916f1ea964f83551f95;hp=2d391082f83ee5299c771d6b6c9d90c4eec7c786;hpb=998f8c437ca6ea5f76e261ef544e90ebee632f78;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2d39108..fe6f4cf 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -48,13 +48,17 @@ public class AlignFrame
     extends GAlignFrame implements DropTargetListener, FeatureListener
 {
   /** DOCUMENT ME!! */
-  public static final int NEW_WINDOW_WIDTH = 700;
+  public static final int DEFAULT_WIDTH = 700;
 
   /** DOCUMENT ME!! */
-  public static final int NEW_WINDOW_HEIGHT = 500;
-  AlignmentPanel alignPanel;
+  public static final int DEFAULT_HEIGHT = 500;
+  public AlignmentPanel alignPanel;
   AlignViewport viewport;
 
+
+  Vector alignPanels = new Vector();
+
+
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
   Stack historyList = new Stack();
@@ -62,17 +66,56 @@ public class AlignFrame
   private int treeCount = 0;
 
   /**
+   * Creates a new AlignFrame object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignFrame(AlignmentI al, int width, int height)
+  {
+    this(al, null, width, height);
+  }
+
+
+  /**
    * new alignment window with hidden columns
    * @param al AlignmentI
    * @param hiddenColumns ColumnSelection or null
    */
-  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
-
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
+                    int width, int height)
+  {
+    this.setSize(width, height);
     viewport = new AlignViewport(al, hiddenColumns);
 
+    alignPanel = new AlignmentPanel(this, viewport);
+
+    if(al.getDataset()==null)
+    {
+      al.setDataset(null);
+    }
+
+    addAlignmentPanel(alignPanel);
+    init();
+  }
+
+  /**
+   * Make a new AlignFrame from exisiting alignmentPanels
+   * @param ap AlignmentPanel
+   * @param av AlignViewport
+   */
+  public AlignFrame(AlignmentPanel ap)
+  {
+    viewport = ap.av;
+    alignPanel = ap;
+    addAlignmentPanel(ap);
+    init();
+  }
+
+  void init()
+  {
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
-    if(viewport.vconsensus==null)
+    if (viewport.hconsensus == null)
     {
       //Out of memory calculating consensus.
       BLOSUM62Colour.setEnabled(false);
@@ -83,73 +126,315 @@ public class AlignFrame
       modifyPID.setEnabled(false);
     }
 
-    alignPanel = new AlignmentPanel(this, viewport);
-
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
-    if(sortby.equals("Id"))
+    if (sortby.equals("Id"))
       sortIDMenuItem_actionPerformed(null);
-    else if(sortby.equals("Pairwise Identity"))
+    else if (sortby.equals("Pairwise Identity"))
       sortPairwiseMenuItem_actionPerformed(null);
 
-   // remove(tabbedPane);
-    getContentPane().add(alignPanel, BorderLayout.CENTER);
+    if (Desktop.desktop != null)
+   {
+     addServiceListeners();
+     setGUINucleotide(viewport.alignment.isNucleotide());
+   }
+
+   if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+   {
+     wrapMenuItem.setSelected(true);
+     wrapMenuItem_actionPerformed(null);
+   }
 
+   addKeyListener();
+  }
 
+  void addKeyListener()
+  {
+      final AlignFrame af = this;
+      addKeyListener(new KeyAdapter()
+      {
+        public void keyPressed(KeyEvent evt)
+        {
+          if (viewport.cursorMode
+              && evt.getKeyCode() >= KeyEvent.VK_0
+              && evt.getKeyCode() <= KeyEvent.VK_9)
+          {
+            alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+          }
+
+          switch (evt.getKeyCode())
+          {
+            case KeyEvent.VK_V:
+              if (!evt.isControlDown())
+              {
+                AlignmentI al;
+                if(viewport.hasHiddenRows)
+                {
+                  al = viewport.alignment.getHiddenSequences().getFullAlignment();
+                }
+                else
+                  al = new Alignment(viewport.alignment.getSequencesArray());
 
-  //  tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+                AlignViewport newview = new AlignViewport(al);
 
-    ///Dataset tab
-    /////////////////////////
-    if(al.getDataset()==null)
+                AlignmentPanel copy = new AlignmentPanel(af, newview);
+
+                if(viewport.viewName==null)
+                  viewport.viewName="View 1";
+
+                copy.av.sequenceSetID = viewport.getSequenceSetId();
+                copy.av.viewName = "View " +
+                    (Desktop.getViewCount(viewport.getSequenceSetId())+1);
+
+
+                addAlignmentPanel(copy);
+                PaintRefresher.Register(copy, viewport.getSequenceSetId());
+                PaintRefresher.Register(alignPanel,
+                                        viewport.getSequenceSetId());
+
+              }
+              break;
+            case KeyEvent.VK_G:
+              Desktop.instance.gatherViews(af);
+              break;
+
+            case KeyEvent.VK_X:
+              if (!evt.isControlDown())
+              {
+                Desktop.instance.explodeViews(af);
+              }
+              break;
+
+
+            case 27: // escape key
+              deselectAllSequenceMenuItem_actionPerformed(null);
+
+              break;
+
+            case KeyEvent.VK_DOWN:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.moveCursor(0, 1);
+              }
+              else
+                moveSelectedSequences(false);
+              break;
+
+            case KeyEvent.VK_UP:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.moveCursor(0, -1);
+              }
+              else
+                moveSelectedSequences(true);
+              break;
+
+            case KeyEvent.VK_LEFT:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.moveCursor( -1, 0);
+              }
+              break;
+
+            case KeyEvent.VK_RIGHT:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.moveCursor(1, 0);
+              }
+              break;
+
+            case KeyEvent.VK_SPACE:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+                                           || evt.isShiftDown()
+                                           || evt.isAltDown());
+              }
+              break;
+
+            case KeyEvent.VK_DELETE:
+            case KeyEvent.VK_BACK_SPACE:
+              if (!viewport.cursorMode)
+              {
+                cut_actionPerformed(null);
+              }
+              else
+                alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+                                           || evt.isShiftDown()
+                                           || evt.isAltDown());
+
+              break;
+
+            case KeyEvent.VK_S:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorRow();
+              }
+              break;
+            case KeyEvent.VK_C:
+              if (viewport.cursorMode && !evt.isControlDown())
+              {
+                alignPanel.seqPanel.setCursorColumn();
+              }
+              break;
+            case KeyEvent.VK_P:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorPosition();
+              }
+              break;
+
+            case KeyEvent.VK_ENTER:
+            case KeyEvent.VK_COMMA:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setCursorRowAndColumn();
+              }
+              break;
+
+            case KeyEvent.VK_Q:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+              }
+              break;
+            case KeyEvent.VK_M:
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+              }
+              break;
+
+            case KeyEvent.VK_F2:
+              viewport.cursorMode = !viewport.cursorMode;
+              statusBar.setText("Keyboard editing mode is " +
+                                           (viewport.cursorMode ? "on" : "off"));
+              if (viewport.cursorMode)
+              {
+                alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
+                alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+              }
+              alignPanel.seqPanel.seqCanvas.repaint();
+              break;
+
+            case KeyEvent.VK_F1:
+              try
+              {
+                ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
+                java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
+                javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
+
+                javax.help.HelpBroker hb = hs.createHelpBroker();
+                hb.setCurrentID("home");
+                hb.setDisplayed(true);
+              }
+              catch (Exception ex)
+              {
+                ex.printStackTrace();
+              }
+              break
+                  ;
+            case KeyEvent.VK_H:
+            {
+              boolean toggleSeqs = !evt.isControlDown();
+              boolean toggleCols = !evt.isShiftDown();
+
+              boolean hide = false;
+
+              SequenceGroup sg = viewport.getSelectionGroup();
+              if (toggleSeqs)
+              {
+                if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())
+                {
+                  hideSelSequences_actionPerformed(null);
+                  hide = true;
+                }
+                else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))
+                  showAllSeqs_actionPerformed(null);
+              }
+
+              if (toggleCols)
+              {
+                if (viewport.colSel.getSelected().size() > 0)
+                {
+                  hideSelColumns_actionPerformed(null);
+                  if (!toggleSeqs)
+                    viewport.selectionGroup = sg;
+                }
+                else if (!hide)
+                  showAllColumns_actionPerformed(null);
+              }
+              break;
+            }
+            case KeyEvent.VK_PAGE_UP:
+              if (viewport.wrapAlignment)
+                alignPanel.scrollUp(true);
+              else
+                alignPanel.setScrollValues(viewport.startRes,
+                                           viewport.startSeq
+                                           - viewport.endSeq + viewport.startSeq);
+              break;
+            case KeyEvent.VK_PAGE_DOWN:
+              if (viewport.wrapAlignment)
+                alignPanel.scrollUp(false);
+              else
+                alignPanel.setScrollValues(viewport.startRes,
+                                           viewport.startSeq
+                                           + viewport.endSeq - viewport.startSeq);
+              break;
+
+
+          }
+        }
+      });
+  }
+
+
+  public void addAlignmentPanel(final AlignmentPanel ap)
+  {
+    alignPanels.addElement(ap);
+
+    int aSize = alignPanels.size();
+
+   tabbedPane.setVisible(aSize>1 || ap.av.viewName!=null);
+
+    if (aSize == 1 && ap.av.viewName==null)
     {
-      al.setDataset(null);
+      this.getContentPane().add(ap, BorderLayout.CENTER);
     }
-   // AlignViewport ds = new AlignViewport(al.getDataset(), true);
-   // AlignmentPanel dap = new AlignmentPanel(this, ds);
-  //  tabbedPane.add("Dataset", dap);
-  //  viewports.add(ds);
-  //  alignPanels.add(dap);
-    /////////////////////////
+    else
+    {
+      if (aSize == 2)
+      {
+        AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+        tabbedPane.addTab(first.av.viewName==null?"Original":first.av.viewName,first);
 
+        this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
+      }
+
+      tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap);
+    }
 
-    viewport.addPropertyChangeListener(new PropertyChangeListener()
+    ap.av.updateConsensus(ap);
+    ap.av.updateConservation(ap);
+
+
+    ap.av.addPropertyChangeListener(new PropertyChangeListener()
     {
      public void propertyChange(PropertyChangeEvent evt)
      {
        if (evt.getPropertyName().equals("alignment"))
        {
+         PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
          alignmentChanged();
        }
      }
    });
 
-
-    if (Desktop.desktop != null)
-    {
-      addServiceListeners();
-      setGUINucleotide(al.isNucleotide());
-    }
-
-
-    if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
-    {
-      wrapMenuItem.setSelected(true);
-      wrapMenuItem_actionPerformed(null);
-    }
-
   }
 
 
-  /**
-   * Creates a new AlignFrame object.
-   *
-   * @param al DOCUMENT ME!
-   */
-  public AlignFrame(AlignmentI al)
-  {
-    this(al, null);
-  }
+
 
   public AlignViewport getViewport()
   {
@@ -175,6 +460,7 @@ public class AlignFrame
         }
       }
     });
+
     addInternalFrameListener(new javax.swing.event.
                              InternalFrameAdapter()
     {
@@ -518,6 +804,7 @@ public class AlignFrame
 
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -527,7 +814,14 @@ public class AlignFrame
   {
     try
     {
-      PaintRefresher.components.remove(viewport.alignment);
+      for(int i=0; i<alignPanels.size(); i++)
+      {
+        AlignmentPanel ap = (AlignmentPanel)alignPanels.elementAt(i);
+        PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
+        PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
+        PaintRefresher.RemoveComponent(ap);
+      }
+
       this.setClosed(true);
     }
     catch (Exception ex)
@@ -535,12 +829,13 @@ public class AlignFrame
     }
   }
 
+
   /**
    * DOCUMENT ME!
    */
   void updateEditMenuBar()
   {
-    if (historyList.size() > 0)
+  /*  if (historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
 
@@ -564,7 +859,7 @@ public class AlignFrame
     {
       redoMenuItem.setEnabled(false);
       redoMenuItem.setText("Redo");
-    }
+    }*/
   }
 
   /**
@@ -604,7 +899,7 @@ public class AlignFrame
   {
     HistoryItem nh,hi = (HistoryItem) redoList.pop();
     historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment,
-        HistoryItem.HIDE)); 
+        HistoryItem.HIDE));
     if (hi.alColumnChanges!=null)
       nh.alColumnChanges=hi.alColumnChanges.getInverse();
     restoreHistoryItem(hi);
@@ -695,6 +990,7 @@ public class AlignFrame
    */
   protected void copy_actionPerformed(ActionEvent e)
   {
+    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -713,9 +1009,36 @@ public class AlignFrame
         seqs,
         omitHidden);
 
+    StringSelection ss = new StringSelection(output);
+
+    try
+    {
+      //Its really worth setting the clipboard contents
+      //to empty before setting the large StringSelection!!
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+          .setContents(new StringSelection(""), null);
+
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+          .setContents(ss, Desktop.instance);
+    }
+    catch (OutOfMemoryError er)
+    {
+      er.printStackTrace();
+      javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Out of memory copying region!!"
+                  +
+                  "\nSee help files for increasing Java Virtual Machine memory."
+                  , "Out of memory",
+                  javax.swing.JOptionPane.WARNING_MESSAGE);
+            }
+          });
 
-    Toolkit.getDefaultToolkit().getSystemClipboard()
-        .setContents(new StringSelection(output), Desktop.instance);
+      return;
+    }
 
     Vector hiddenColumns = null;
     if(viewport.hasHiddenColumns)
@@ -732,9 +1055,12 @@ public class AlignFrame
       }
     }
 
+
+
     Desktop.jalviewClipboard = new Object[]{ seqs,
         viewport.alignment.getDataset(),
         hiddenColumns};
+    statusBar.setText("Copied "+seqs.length+" sequences to clipboard.");
   }
 
   /**
@@ -776,11 +1102,35 @@ public class AlignFrame
         return;
       }
 
-      String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
-      if(str.length()<1)
+      String str, format;
+      try
+      {
+        str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+        if (str.length() < 1)
+          return;
+
+        format = new IdentifyFile().Identify(str, "Paste");
+
+      }
+      catch (OutOfMemoryError er)
+      {
+        er.printStackTrace();
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory pasting sequences!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+
         return;
+      }
 
-      String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
 
@@ -799,13 +1149,12 @@ public class AlignFrame
 
       if (newAlignment)
       {
-        alignment = new Alignment(sequences);
-
-        if(Desktop.jalviewClipboard!=null)
-           alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
-        else
-           alignment.setDataset( null );
+          alignment = new Alignment(sequences);
 
+          if (Desktop.jalviewClipboard != null)
+            alignment.setDataset( (Alignment) Desktop.jalviewClipboard[1]);
+          else
+            alignment.setDataset(null);
       }
       else
       {
@@ -819,6 +1168,9 @@ public class AlignFrame
               sequences[i].getEnd());
 
           alignment.addSequence(newseq);
+          PaintRefresher.Refresh(alignPanel,
+                                 alignPanel.av.getSequenceSetId(),
+                                 null,newseq);
         }
 
 
@@ -829,8 +1181,6 @@ public class AlignFrame
 
 
 
-
-
       // Add any annotations attached to sequences
       for (int i = 0; i < sequences.length; i++)
      {
@@ -862,7 +1212,7 @@ public class AlignFrame
 
      if(newAlignment)
      {
-       AlignFrame af = new AlignFrame(alignment);
+       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT);
        String newtitle = new String("Copied sequences");
 
        if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
@@ -890,8 +1240,8 @@ public class AlignFrame
          newtitle = newtitle.concat("- from " + title);
        }
 
-       Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                NEW_WINDOW_HEIGHT);
+       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
+                                DEFAULT_HEIGHT);
 
      }
 
@@ -935,33 +1285,6 @@ public class AlignFrame
     SequenceGroup sg = viewport.getSelectionGroup();
 
 
-
-    //Jalview no longer allows deletion of residues.
-    //Check here whether any residues are in selection area
-   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
-    {
-      for (int i = 0; i < sg.sequences.size(); i++)
-      {
-        SequenceI seq = sg.getSequenceAt(i);
-        int j = sg.getStartRes();
-        do
-        {
-          if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
-          {
-            JOptionPane.showInternalMessageDialog(
-                Desktop.desktop, "Cannot delete residues from alignment!\n"
-                + "Try hiding columns instead.",
-                "Deletion of residues not permitted",
-                JOptionPane.WARNING_MESSAGE);
-
-            return;
-          }
-          j++;
-        }while(j<=sg.getEndRes());
-      }
-    }*/
-
-
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
                                    HistoryItem.HIDE));
 
@@ -969,8 +1292,6 @@ public class AlignFrame
     for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
@@ -983,10 +1304,7 @@ public class AlignFrame
       if (seq.getSequence().length() < 1)
       {
         viewport.getAlignment().deleteSequence(seq);
-      }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
+        PaintRefresher.Refresh(alignPanel,alignPanel.av.getSequenceSetId(),seq,null);
       }
     }
 
@@ -1019,6 +1337,7 @@ public class AlignFrame
   {
     viewport.alignment.deleteAllGroups();
     viewport.setSelectionGroup(null);
+    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
     alignPanel.repaint();
   }
 
@@ -1039,7 +1358,8 @@ public class AlignFrame
 
     sg.setEndRes(viewport.alignment.getWidth() - 1);
     viewport.setSelectionGroup(sg);
-    PaintRefresher.Refresh(null, viewport.alignment);
+    alignPanel.repaint();
+    PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
   /**
@@ -1060,7 +1380,7 @@ public class AlignFrame
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.repaint();
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
   }
 
   /**
@@ -1085,7 +1405,7 @@ public class AlignFrame
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    PaintRefresher.Refresh(null, viewport.alignment);
+    PaintRefresher.Refresh(this, viewport.getSequenceSetId());
   }
 
   public void invertColSel_actionPerformed(ActionEvent e)
@@ -1192,10 +1512,11 @@ public class AlignFrame
     ShiftList shifts;
     viewport.getAlignment().removeGaps(shifts=new ShiftList());
     edit.alColumnChanges=shifts.getInverse();
-    if (viewport.hasHiddenColumns) 
+    if (viewport.hasHiddenColumns)
       viewport.getColumnSelection().compensateForEdits(shifts);
     viewport.setStartRes(seq.findIndex(startRes)-1);
    viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
   }
 
   /**
@@ -1217,7 +1538,6 @@ public class AlignFrame
 
 
     SequenceI current;
-    int jSize;
 
     Vector seqs = null;
 
@@ -1247,13 +1567,13 @@ public class AlignFrame
        current = (SequenceI) seqs.elementAt(i);
        //dr[i]=
        current.removeGaps(start, end);
-       /*if (d<diff) // can only shift 
+       /*if (d<diff) // can only shift
          diff=d;
        if (diffmax<d)
          diffmax=d;
          */
      }
-     /* // after the end of each chunk - 
+     /* // after the end of each chunk -
       * if (diff>0) {
       // record shift for history.
        editgaps.addShift(start, diff);
@@ -1266,38 +1586,47 @@ public class AlignFrame
         current = (SequenceI) seqs.elementAt(i);
         if (dr[i]-diff>0) {
         String sq = current.getSequence();
-        current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); 
+        current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring());
         }
         }
-       } 
+       }
        }*/
 
     viewport.setStartRes(seq.findIndex(startRes)-1);
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
   }
 
  public void alignmentChanged()
  {
-   if(viewport.padGaps)
-     viewport.getAlignment().padGaps();
+   AlignViewport av;
+   AlignmentPanel ap;
 
-   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
+   for(int i=0; i<alignPanels.size(); i++)
    {
-     viewport.updateConsensus();
-     viewport.updateConservation();
-   }
+     ap = (AlignmentPanel) alignPanels.elementAt(i);
+     av = ap.av;
+
+   if (av.padGaps)
+       av.getAlignment().padGaps();
 
-   resetAllColourSchemes();
-   if(alignPanel.overviewPanel!=null)
-     alignPanel.overviewPanel.updateOverviewImage();
+     if (av.hconsensus != null && av.autoCalculateConsensus)
+     {
+       av.updateConsensus(ap);
+       av.updateConservation(ap);
+       ap.annotationPanel.repaint();
+     }
+
+     resetAllColourSchemes();
 
-   viewport.alignment.adjustSequenceAnnotations();
+     av.alignment.adjustSequenceAnnotations();
 
-   if(alignPanel.overviewPanel!=null)
-     alignPanel.overviewPanel.updateOverviewImage();
+     if (ap.overviewPanel != null)
+       ap.overviewPanel.updateOverviewImage();
 
-   alignPanel.repaint();
+     ap.repaint();
+   }
  }
 
   void resetAllColourSchemes()
@@ -1312,7 +1641,7 @@ public class AlignFrame
                           viewport.alignment.getWidth());
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
       if (cs.conservationApplied())
       {
         Alignment al = (Alignment) viewport.alignment;
@@ -1352,8 +1681,9 @@ public class AlignFrame
 
     viewport.padGaps = padGapsMenuitem.isSelected();
 
-   // if (viewport.padGaps)
-    alignmentChanged();
+    viewport.firePropertyChange("alignment",
+                                null,
+                                viewport.getAlignment().getSequences());
   }
 
   /**
@@ -1441,6 +1771,7 @@ public class AlignFrame
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
+    alignPanel.repaint();
   }
 
   public void hideSelColumns_actionPerformed(ActionEvent e)
@@ -1756,7 +2087,7 @@ public class AlignFrame
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.vconsensus);
+      cs.setConsensus(viewport.hconsensus);
     }
 
     viewport.setGlobalColourScheme(cs);
@@ -2110,7 +2441,9 @@ public class AlignFrame
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
     if(viewport.autoCalculateConsensus)
     {
-      alignmentChanged();
+      viewport.firePropertyChange("alignment",
+                                  null,
+                                  viewport.getAlignment().getSequences());
     }
   }
 
@@ -2166,9 +2499,15 @@ public class AlignFrame
   {
     TreePanel tp;
 
-    if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize(false) > 3))
-    {
+    if (viewport.getSelectionGroup() != null) {
+      if (viewport.getSelectionGroup().getSize(false) < 3) {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "You need to have more than two sequences selected to build a tree!",
+                                      "Not enough sequences",
+                                      JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
       int s = 0;
       SequenceGroup sg = viewport.getSelectionGroup();
 
@@ -2190,7 +2529,7 @@ public class AlignFrame
       }
 
       title = title + " on region";
-      tp = new TreePanel(viewport, type, pwType);
+      tp = new TreePanel(alignPanel, type, pwType);
     }
     else
     {
@@ -2210,7 +2549,7 @@ public class AlignFrame
       if(viewport.alignment.getHeight()<2)
         return;
 
-      tp = new TreePanel(viewport, type, pwType);
+      tp = new TreePanel(alignPanel, type, pwType);
     }
 
     addTreeMenuItem(tp, title);
@@ -2406,16 +2745,26 @@ public class AlignFrame
   {
     return ShowNewickTree(nf,title,600,500,4,5);
   }
+  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input)
+  {
+    return ShowNewickTree(nf,title, input, 600,500,4,5);
+  }
+  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y) {
+    return ShowNewickTree(nf, title, null, w, h, x, y);
+  }
   /**
-   * DOCUMENT ME!
-   *
-   * @param nf DOCUMENT ME!
-   * @param title DOCUMENT ME!
+   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
    *
-   * @return DOCUMENT ME!
+   * @param nf the tree
+   * @param title tree viewer title
+   * @param input Associated alignment input data (or null)
+   * @param w width
+   * @param h height
+   * @param x position
+   * @param y position
+   * @return TreePanel handle
    */
-  public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
-  {
+  public TreePanel ShowNewickTree(NewickFile nf, String title, AlignmentView input, int w,int h,int x, int y) {
     TreePanel tp = null;
 
     try
@@ -2424,10 +2773,10 @@ public class AlignFrame
 
       if (nf.getTree() != null)
       {
-        tp = new TreePanel(viewport,
+        tp = new TreePanel(alignPanel,
                            "FromFile",
                            title,
-                           nf);
+                           nf, input);
 
         tp.setSize(w,h);
 
@@ -2543,7 +2892,7 @@ public class AlignFrame
               if (msa.getSequences().length == 1)
               {
                 // Single Sequence prediction
-                new jalview.ws.JPredClient(sh, title, false, msa, af);
+                new jalview.ws.JPredClient(sh, title, false, msa, af, true);
               }
               else
               {
@@ -2551,7 +2900,7 @@ public class AlignFrame
                 {
                   // Sequence profile based prediction
                   new jalview.ws.JPredClient(sh,
-                      title, true, msa, af);
+                      title, true, msa, af, true);
                 }
               }
             }
@@ -2678,39 +3027,16 @@ public void showTranslation_actionPerformed(ActionEvent e)
     }
   }
 
-    AlignFrame af = new AlignFrame(al);
+    AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
-                             NEW_WINDOW_WIDTH,
-                             NEW_WINDOW_HEIGHT);
-
+                             DEFAULT_WIDTH,
+                             DEFAULT_HEIGHT);
 
-   // AlignViewport newViewport = new AlignViewport(al);
-   // AlignmentPanel ap = new AlignmentPanel(this, newViewport);
-   // tabbedPane.add("Protein", ap);
-   // viewports.add(newViewport);
-  //  alignPanels.add(ap);
 
-    ///Dataset tab
-  /////////////////////////
-
-  //  AlignViewport ds = new AlignViewport(al.getDataset());
-  //  ds.setDataset(true);
-  //  AlignmentPanel dap = new AlignmentPanel(this, ds);
-  //  tabbedPane.add("Dataset", dap);
-  //  viewports.add(ds);
-  //  alignPanels.add(dap);
-  /////////////////////////
 
 
 }
 
-/*public void tabSelected()
- {
-  int index = tabbedPane.getSelectedIndex();
-  viewport = (AlignViewport)viewports.elementAt(index);
-  alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
- }*/
-
 /**
  * DOCUMENT ME!
  *
@@ -2818,17 +3144,35 @@ public void drop(DropTargetDropEvent evt)
    public void loadJalviewDataFile(String file)
   {
     try{
+      String protocol = "File";
+
+      if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+      {
+        protocol = "URL";
+      }
+
       boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
           alignment, file);
 
       if (!isAnnotation)
       {
-        boolean isGroupsFile = parseFeaturesFile(file,
-                                                AppletFormatAdapter.FILE);
+        boolean isGroupsFile = parseFeaturesFile(file,protocol);
         if (!isGroupsFile)
         {
-          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
-          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
+          String format = new IdentifyFile().Identify(file, protocol);
+
+          if(format.equalsIgnoreCase("JnetFile"))
+          {
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                file, protocol);
+            new JnetAnnotationMaker().add_annotation(predictions,
+                viewport.getAlignment(),
+                0, false);
+            alignPanel.adjustAnnotationHeight();
+            alignPanel.repaint();
+          }
+          else
+            new FileLoader().LoadFile(viewport, file, protocol, format);
         }
       }
       else
@@ -2842,4 +3186,36 @@ public void drop(DropTargetDropEvent evt)
       ex.printStackTrace();
     }
   }
+
+  public void tabSelectionChanged(int index)
+  {
+    if (index > -1)
+    {
+      alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+      viewport = alignPanel.av;
+    }
+  }
+
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+    if(SwingUtilities.isRightMouseButton(e))
+    {
+      String reply = JOptionPane.showInternalInputDialog(this,
+          "Enter View Name",
+          "Edit View Name",
+          JOptionPane.QUESTION_MESSAGE);
+
+      if (reply != null)
+      {
+        viewport.viewName = reply;
+        tabbedPane.setTitleAt( tabbedPane.getSelectedIndex() ,reply);
+      }
+    }
+  }
+
+
+  public AlignViewport getCurrentView()
+  {
+    return viewport;
+  }
 }